Main
Danang Crysnanto
Interested in the bioinformatics of the large-scale whole-genome sequencing data. Current work first to propose the transition from linear to more representative, graph-based reference genome for unbiased sequence variant analysis.
Education
PhD Candidate in Computational Animal Genomics
Zurich Switzerland
Swiss Federal Institute of Technology (ETH Zurich)
Current - 2018
- Research project: Graph-based genomic analysis
- Skills learned: Graph analytics, Bioinformatics pipeline management
- Adviser: Prof.Dr. Hubert Pausch
Msc in Quantitative Genetics and Genome Analysis
Edinburgh United Kingdom
The University of Edinburgh
2017 - 2016
- Thesis: Widespread gene duplication in Drosophila RNAi pathways
- Skills learned: Pylogenetic analysis, Bayesian statistics
- Adviser: Dr. Darren Obbard
- Best master thesis with distinction (all marks > 85)
Selected Publications
Accurate sequence variant genotyping in cattle using variation-aware genome graphs
Genetic Selection Evolution
N/A
2019
- Danang Crysnanto and Hubert Pausch
- Published in the first year of PhD
- First work of using graphs for sequence variant discovery in livestock
Widespread gene duplication and adaptive evolution in the RNA-interference pathways of the Drosophila obscura group
BMC Evolutionary Biology
N/A
2019
- Danang Crysnanto and Daren Obbard
- Published from Master’s work
- Identified massive gene duplications from analysis >30 Drosophila genome
Selected awards
Sir Kenneth Mather Memorial Prize
N/A
The Genetics Society
2018
- Awarded annually based on the UK BSc, Msc and PhD thesis with an outstanding work in population genomics and quantitative genetics.
The Douglas Falconer Prize
N/A
The University of Edinburgh
2017
- Awarded as the best Master’s thesis in the area of population genomics and quantitative genetics
Bronze Medalist 21st International Biology Olympiad (IBO)
Changwon South Korea
International Biology Olympiad
2010
- International biology competition for high school students from 60 countries, who are winners of their respective National Biology Olympiad.
Selected conference and talks
Plant and Animal Genome (PAG) Conference
San Diego USA
N/A
2020
- Talk title: Mapping sequencing read to bovine genome graph
Computational PANgenomics
Oeiras Portugal
Gulbekian Training Program in Bioinformatics
2019
- Training with mini-hackaton on graph genomics
Genome Informatics and Livestock Genomics Conference
Cambridge United Kingdom
N/A
2018
- Talk title: Assessment of the graph-based genotyping with bovine short-read data
52nd Population Genetics Group Conference
Oxford United Kingdom
N/A
2018
- Talk title:Widespread gene duplication in Drosophila immune pathways (Invited talk)
Selected training
Nextflow for reproducible genomics
Tubingen Germany
Quantitative Biology Center (QBIC)
2019
- Workshop on implementation of reproducible genomics
R packages
Swiss Institute of Bioinformatics
University of Zurich
2019
- Training on creating R packages using devtools
Basic Tensorflow
Lausanne Switzerland
Google Zurich
2019
- Training on basic machine learning in Swiss Applied Machine Learning Days
Docker for reproducible computational research
Swiss Institute of Bioinformatics
University of Bern
2018
- Training on reproducibility genomic analysis using Docker
Bioinformatics of Long-Range Sequencing
Swiss Institute of Bioinformatics
University of Zurich
2018
- Training on long-read (Pacbio and Nanopore) data analysis
Python for Life Science
Edinburgh United Kingdom
Edinburgh Genomics
2017
- Using Python data science stack (e.g., Pandas, Jupyter) for genomics data analysis
High performance computing for genomics application
Scientific IT Services
ETH Zurich
2017
- Training on best practice of using ETH big data clusterfor genomic application
GATK Best Practice for Genomic Data Analysis
Broad Institute
Harvard MA USA
2017
- Training on the best practice variant discovery with Genomic analysis toolkit (GATK)